annotate xcms_merge.r @ 11:772290533d6e draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8ed93601e09e1db2fbaef5af29d58464b639f2a8

#!/usr/bin/env Rscript

#Import the different functions
source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
source_local("lib.r")

pkgs <- c("xcms","batch")
loadAndDisplayPackages(pkgs)
cat("\n\n");

args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects


cat("\tXSET MERGING...\n")

mergeXDataReturn <- mergeXData(args)
xdata <- mergeXDataReturn$xdata
singlefile <- mergeXDataReturn$singlefile
md5sumList <- mergeXDataReturn$md5sumList
sampleNamesList <- mergeXDataReturn$sampleNamesList
chromTIC <- mergeXDataReturn$chromTIC
chromBPI <- mergeXDataReturn$chromBPI

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

cat("\n\n")

cat("\tXCMSnExp OBJECT INFO\n")
print(pData(xdata))
print(xdata)
cat("\n\n")

cat("\txcmsSet OBJECT INFO\n")
# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)
print(xset@phenoData)
print(xset)
cat("\n\n")

cat("\tSAVE RData\n")
#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI")
save(list=objects2save[objects2save %in% ls()], file="merged.RData")